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The combination of an ultracold ion source based on photoionization of a laser-cooled gas and time-dependent acceleration fields enables precise manipulation of ion beams. We demonstrate reduction in the longitudinal energy spread and transverse (de)focusing of the beam by applying time-dependent acceleration voltages. In addition, we show how time-dependent acceleration fields can be used to control both the sign and strength of the spherical aberrations. The experimental results are in close agreement with detailed charged particle tracking simulations and can be explained in terms of a simple analytical model.